Socrates -
SOft Clip re-alignment To idEntify Structural variants

Developed by Arthur Hsu, Jan Schroeder and Tony Papenfuss

Introduction

Socrates is a highly efficient and sensitive method for detecting genomic rearrangements in tumours that utilises split-read data. Socrates features single nucleotide resolution, high sensitivity, and high specificity in simulated data. It annotates micro-homologies and untemplated sequence insertions at the breakpoint. It takes advantage of parallelism for efficient use of resources.

The latest version of Socrates (version 1.1+) is available from github. It requires Java 1.8. Older versions are also available. They will run with older versions of Java.

Socrates is a pure split read-based breakpoint caller, which is designed to be fast and sensitive.
It is a highly efficient for detecting genomic rearrangements in tumours, but requires downstream
filtering of calls by the user.